Nucleotide Excision Repair Pathway

The inability to repair DNA damage properly leads to various disorders and enhanced rates of tumor development. Mammals respond to chromosomal insults by activating a complex damage response pathway. These pathways regulate known responses such as cell cycle arrest and apoptosis, and have recently been shown to control additional processes including direct activation of DNA repair networks (Ref.1). Different DNA-repair pathways operate on different types of DNA lesions. NER (Nucleotide Excision Repair) is the most flexible of the DNA repair pathways considering the diversity of DNA lesions it acts upon. The most significant of these lesions are pyrimidine dimers caused by the UV component of sunlight. Other NER substrates include bulky chemical adducts, DNA intrastrand cross links, and some forms of oxidative damage. The common features of lesions recognized by the NER pathway are that they cause both a helical distortion of the DNA duplex and a modification of the DNA chemistry (Ref.2).

The NER process requires the action of more than 30 proteins in a stepwise manner that includes damage recognition, local opening of the DNA duplex around the lesion, dual incision of the damaged DNA strand, gap repair synthesis, and strand ligation. There are two distinct forms of NER: GG-NER (Global Genomic NER), which corrects damage in transcriptionally silent areas of the genome, and TC-NER (Transcription Coupled NER), which repairs lesions on the actively transcribed strand of the DNA. These two subpathways are fundamentally identical except in their mechanism of damage recognition. In GG-NER, the XPC (Xeroderma Pigmentosum, Complementation Group C) protein complex is responsible for the initial detection of damaged DNA (Ref.5). Conversely, damage recognition during TC-NER does not require XPC, but occurs when the transcription machinery is stalled at the site of injury. The stalled RNA Polymerase complex is displaced in order to allow the NER proteins to access the damaged DNA. This displacement is aided by the action of the CSA (Cockayne Syndrome A) and CSB proteins, as well as other TC-NER-specific factors. The subsequent steps of GG- and TC-NER proceed in an essentially identical manner. XPA and the heterotrimeric RPA (Replication Protein A) then bind at the site of injury and further aid in damage recognition. Next, the XPB and XPD helicases, components of the multi-subunit Transcription Factor, TFIIH, unwind the DNA duplex in the immediate vicinity of the lesion for the enzyme RNA Polymerase-II to begin transcription. The Endonucleases XPG and ERCC1 (Excision Repair Cross-Complementing Group-1)/XPF then cleave one strand of the DNA at positions 3' and 5' to the damage, respectively, generating an approximately 30 base oligonucleotide containing the lesion. This oligonucleotide is displaced, making way for gap repair synthesis (performed by DNA Pol Delta/Epsilon, as well as several replication accessory factors). Finally the nick in the repaired strand is sealed by a DNA Ligase, thus completing the NER process (Ref.3).

NER deals with the wide class of helix-distorting lesions that interfere with base pairing and generally obstruct transcription and normal replication. Most NER lesions arise from exogenous sources (except for some oxidative lesions) (Ref.4). At least three syndromes are associated with inborn defects in NER: XP, CS and TTD (Trichothiodystrophy), all characterized by exquisite sun sensitivity (Ref.5). The prototype repair disorder, XP exhibits a dramatic >1000-fold incidence of sun-induced skin cancer (basal cell carcinoma, squamous cell carcinoma and melanoma). The disorder arises from mutations in one of seven genes (XPA–XPG) (Ref.6). CS, caused by mutation in the CSA or CSB genes, is a TC-NER specific disorder that is remarkably dissimilar from XP. No predisposition to cancer is observed because TC-NER defect causes CS cells to be particularly sensitive to lesion-induced apoptosis, thereby protecting against tumorigenesis. Physical and neurological developments are impaired, resulting in dwarfism and dysmyelination. The syndrome includes features of premature ageing, which is related to the increased trigger for apoptosis induced by transcriptional arrest from endogenous lesions in combination with the TC-NER defect. TTD is a condition sharing many symptoms with CS, but with the additional hallmarks of brittle hair, nails and scaly skin. TTD is not associated with cancer. Mutations in the XPD or XPB genes give rise to all three diseases. Thus, as subunits of TFIIH, XPB and XPD have dual functions: NER and transcription initiation. Mutations not only compromise NER, but also affect transcription, causing developmental delay and reduced expression of the matrix proteins that causes brittle hair and scaly skin (Ref.4).